This was from the Baltimore Sun's interview with Burton. He of course doesn't really explain the ending.

The movie almost has the shape of a concertina -- you get the sense it would take a sequel or two to air all the issues out, including the meaning of the ending.

Burton: "I don't think of sequels per se, but this is the kind of material that circles around on itself. That's what I think people should get from the ending, and why I think they should go with it. What's tied into the mythology of the Planet of the Apes movies is this unsettling quality -- and that's not just from thinking you know where you are and not knowing, but also from finding out that what goes around comes around. You don't ever form a complete circle, but you get this circular structure. Even though I had to build it with snippets and clues, I did think about this film in a way I didn't think about other movies -- about the Big Picture, the circular motion. And maybe 50 percent, maybe 90 percent of that isn't in the movie, but it is definitely underlying the whole thing. I'm not an intellectual, really; I respond to things emotionally. Still, I tried to step back and analyze Planet of the Apes, based on the book and the movies. I started to see an image of the structure: that uncertain, turning-around kind of thing, the going up and the going down. And that's the peculiar beauty of it."